Probabilistic Methods for Bioinformatics

Author: Richard E. Neapolitan
Publisher: Morgan Kaufmann
ISBN: 9780080919362
Format: PDF, ePub
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The Bayesian network is one of the most important architectures for representing and reasoning with multivariate probability distributions. When used in conjunction with specialized informatics, possibilities of real-world applications are achieved. Probabilistic Methods for BioInformatics explains the application of probability and statistics, in particular Bayesian networks, to genetics. This book provides background material on probability, statistics, and genetics, and then moves on to discuss Bayesian networks and applications to bioinformatics. Rather than getting bogged down in proofs and algorithms, probabilistic methods used for biological information and Bayesian networks are explained in an accessible way using applications and case studies. The many useful applications of Bayesian networks that have been developed in the past 10 years are discussed. Forming a review of all the significant work in the field that will arguably become the most prevalent method in biological data analysis. Unique coverage of probabilistic reasoning methods applied to bioinformatics data--those methods that are likely to become the standard analysis tools for bioinformatics. Shares insights about when and why probabilistic methods can and cannot be used effectively; Complete review of Bayesian networks and probabilistic methods with a practical approach.

Probabilistic Modeling in Bioinformatics and Medical Informatics

Author: Dirk Husmeier
Publisher: Springer Science & Business Media
ISBN: 1846281199
Format: PDF, ePub, Mobi
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Probabilistic Modelling in Bioinformatics and Medical Informatics has been written for researchers and students in statistics, machine learning, and the biological sciences. The first part of this book provides a self-contained introduction to the methodology of Bayesian networks. The following parts demonstrate how these methods are applied in bioinformatics and medical informatics. All three fields - the methodology of probabilistic modeling, bioinformatics, and medical informatics - are evolving very quickly. The text should therefore be seen as an introduction, offering both elementary tutorials as well as more advanced applications and case studies.

Foundations of Algorithms

Author: Richard Neapolitan
Publisher: Jones & Bartlett Publishers
ISBN: 1449600166
Format: PDF, ePub, Mobi
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Foundations of Algorithms, Fourth Edition offers a well-balanced presentation of algorithm design, complexity analysis of algorithms, and computational complexity. The volume is accessible to mainstream computer science students who have a background in college algebra and discrete structures. To support their approach, the authors present mathematical concepts using standard English and a simpler notation than is found in most texts. A review of essential mathematical concepts is presented in three appendices. The authors also reinforce the explanations with numerous concrete examples to help students grasp theoretical concepts.

Bayesian Methods in Structural Bioinformatics

Author: Thomas Hamelryck
Publisher: Springer
ISBN: 3642272258
Format: PDF, Docs
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This book is an edited volume, the goal of which is to provide an overview of the current state-of-the-art in statistical methods applied to problems in structural bioinformatics (and in particular protein structure prediction, simulation, experimental structure determination and analysis). It focuses on statistical methods that have a clear interpretation in the framework of statistical physics, rather than ad hoc, black box methods based on neural networks or support vector machines. In addition, the emphasis is on methods that deal with biomolecular structure in atomic detail. The book is highly accessible, and only assumes background knowledge on protein structure, with a minimum of mathematical knowledge. Therefore, the book includes introductory chapters that contain a solid introduction to key topics such as Bayesian statistics and concepts in machine learning and statistical physics.

Learning Bayesian Networks

Author: Richard E. Neapolitan
Publisher: Prentice Hall
ISBN:
Format: PDF, Docs
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For courses in Bayesian Networks or Advanced Networking focusing on Bayesian networks found in departments of Computer Science, Computer Engineering and Electrical Engineering. Also appropriate as a supplementary text in courses on Expert Systems, Machine Learning, and Artificial Intelligence where the topic of Bayesian Networks is covered. This book provides an accessible and unified discussion of Bayesian networks. It includes discussions of topics related to the areas of artificial intelligence, expert systems and decision analysis, the fields in which Bayesian networks are frequently applied. The author discusses both methods for doing inference in Bayesian networks and influence diagrams. The book also covers the Bayesian method for learning the values of discrete and continuous parameters. Both the Bayesian and constraint-based methods for learning structure are discussed in detail.

Bioinformatics

Author: Yu Liu
Publisher: CRC Press
ISBN: 1482246627
Format: PDF, Mobi
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This title includes a number of Open Access chapters. The book introduces bioinformatic and statistical methodology and shows approaches to bias correction and error estimation. It also presents quantitative methods for genome and proteome analysis.

Probabilistic Methods for Financial and Marketing Informatics

Author: Richard E. Neapolitan
Publisher: Elsevier
ISBN: 0080555675
Format: PDF, Docs
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Probabilistic Methods for Financial and Marketing Informatics aims to provide students with insights and a guide explaining how to apply probabilistic reasoning to business problems. Rather than dwelling on rigor, algorithms, and proofs of theorems, the authors concentrate on showing examples and using the software package Netica to represent and solve problems. The book contains unique coverage of probabilistic reasoning topics applied to business problems, including marketing, banking, operations management, and finance. It shares insights about when and why probabilistic methods can and cannot be used effectively. This book is recommended for all R&D professionals and students who are involved with industrial informatics, that is, applying the methodologies of computer science and engineering to business or industry information. This includes computer science and other professionals in the data management and data mining field whose interests are business and marketing information in general, and who want to apply AI and probabilistic methods to their problems in order to better predict how well a product or service will do in a particular market, for instance. Typical fields where this technology is used are in advertising, venture capital decision making, operational risk measurement in any industry, credit scoring, and investment science. Unique coverage of probabilistic reasoning topics applied to business problems, including marketing, banking, operations management, and finance Shares insights about when and why probabilistic methods can and cannot be used effectively Complete review of Bayesian networks and probabilistic methods for those IT professionals new to informatics.

Bayesian Methods for Hackers

Author: Cameron Davidson-Pilon
Publisher: Addison-Wesley Professional
ISBN: 0133902927
Format: PDF, ePub, Docs
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Master Bayesian Inference through Practical Examples and Computation–Without Advanced Mathematical Analysis Bayesian methods of inference are deeply natural and extremely powerful. However, most discussions of Bayesian inference rely on intensely complex mathematical analyses and artificial examples, making it inaccessible to anyone without a strong mathematical background. Now, though, Cameron Davidson-Pilon introduces Bayesian inference from a computational perspective, bridging theory to practice–freeing you to get results using computing power. Bayesian Methods for Hackers illuminates Bayesian inference through probabilistic programming with the powerful PyMC language and the closely related Python tools NumPy, SciPy, and Matplotlib. Using this approach, you can reach effective solutions in small increments, without extensive mathematical intervention. Davidson-Pilon begins by introducing the concepts underlying Bayesian inference, comparing it with other techniques and guiding you through building and training your first Bayesian model. Next, he introduces PyMC through a series of detailed examples and intuitive explanations that have been refined after extensive user feedback. You’ll learn how to use the Markov Chain Monte Carlo algorithm, choose appropriate sample sizes and priors, work with loss functions, and apply Bayesian inference in domains ranging from finance to marketing. Once you’ve mastered these techniques, you’ll constantly turn to this guide for the working PyMC code you need to jumpstart future projects. Coverage includes • Learning the Bayesian “state of mind” and its practical implications • Understanding how computers perform Bayesian inference • Using the PyMC Python library to program Bayesian analyses • Building and debugging models with PyMC • Testing your model’s “goodness of fit” • Opening the “black box” of the Markov Chain Monte Carlo algorithm to see how and why it works • Leveraging the power of the “Law of Large Numbers” • Mastering key concepts, such as clustering, convergence, autocorrelation, and thinning • Using loss functions to measure an estimate’s weaknesses based on your goals and desired outcomes • Selecting appropriate priors and understanding how their influence changes with dataset size • Overcoming the “exploration versus exploitation” dilemma: deciding when “pretty good” is good enough • Using Bayesian inference to improve A/B testing • Solving data science problems when only small amounts of data are available Cameron Davidson-Pilon has worked in many areas of applied mathematics, from the evolutionary dynamics of genes and diseases to stochastic modeling of financial prices. His contributions to the open source community include lifelines, an implementation of survival analysis in Python. Educated at the University of Waterloo and at the Independent University of Moscow, he currently works with the online commerce leader Shopify.

Artificial Intelligence

Author: Richard E. Neapolitan
Publisher: CRC Press
ISBN: 1351384392
Format: PDF, Kindle
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The first edition of this popular textbook, Contemporary Artificial Intelligence, provided an accessible and student friendly introduction to AI. This fully revised and expanded update, Artificial Intelligence: With an Introduction to Machine Learning, Second Edition, retains the same accessibility and problem-solving approach, while providing new material and methods. The book is divided into five sections that focus on the most useful techniques that have emerged from AI. The first section of the book covers logic-based methods, while the second section focuses on probability-based methods. Emergent intelligence is featured in the third section and explores evolutionary computation and methods based on swarm intelligence. The newest section comes next and provides a detailed overview of neural networks and deep learning. The final section of the book focuses on natural language understanding. Suitable for undergraduate and beginning graduate students, this class-tested textbook provides students and other readers with key AI methods and algorithms for solving challenging problems involving systems that behave intelligently in specialized domains such as medical and software diagnostics, financial decision making, speech and text recognition, genetic analysis, and more.

Bayesian Networks in R

Author: Radhakrishnan Nagarajan
Publisher: Springer Science & Business Media
ISBN: 1461464463
Format: PDF, ePub, Docs
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Bayesian Networks in R with Applications in Systems Biology is unique as it introduces the reader to the essential concepts in Bayesian network modeling and inference in conjunction with examples in the open-source statistical environment R. The level of sophistication is also gradually increased across the chapters with exercises and solutions for enhanced understanding for hands-on experimentation of the theory and concepts. The application focuses on systems biology with emphasis on modeling pathways and signaling mechanisms from high-throughput molecular data. Bayesian networks have proven to be especially useful abstractions in this regard. Their usefulness is especially exemplified by their ability to discover new associations in addition to validating known ones across the molecules of interest. It is also expected that the prevalence of publicly available high-throughput biological data sets may encourage the audience to explore investigating novel paradigms using the approaches presented in the book.